Evidence map›Paper›PMID 29183290›Full record

ArticleBMC bioinformatics2017

Modeling, validation and verification of three-dimensional cell-scaffold contacts from terabyte-sized images.

Peter Bajcsy, Soweon Yoon, Stephen J Florczyk, Nathan A Hotaling, Mylene Simon, Piotr M Szczypinski, Nicholas J Schaub, Carl G Simon, Mary Brady, Ram D Sriram

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Review
  3. Review
  4. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Peter BajcsyInformation Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA. peter.bajcsy@nist.gov.ORCID http://orcid.org/0000-0002-6968-2615
Soweon YoonInformation Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Stephen J FlorczykMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Nathan A HotalingNational Eye Institute, National Institute of Health, Bethesda, MD, USA. nathan.hotaling@nih.gov.
Mylene SimonInformation Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Piotr M SzczypinskiLodz University of Technology, Łódź, Poland.
Nicholas J SchaubMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Carl G SimonMaterial Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Mary BradyInformation Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Ram D SriramInformation Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.

Funding

Tissue Engineering and RegenerationT32DE007057 · NIDCR · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI DAVID H. KOHN · 1985 to 2026
$17.3M
PREPARATION AND DISTRUBUTION OF ADULT STEM CELLS: HUMAN &RODENTP40RR017447 · NCRR · TULANE UNIVERSITY OF LOUISIANA · PI PROCKOP, DARWIN JOHNSON · 2003 to 2011
$8.9M
National Center for Research Resources NCRR-NIH P40RR017447NCRR NIH HHS P40 RR017447NIDCR NIH HHS T32 DE007057
6 · The paper itself

Abstract

backgroundCell-scaffold contact measurements are derived from pairs of co-registered volumetric fluorescent confocal laser scanning microscopy (CLSM) images (z-stacks) of stained cells and three types of scaffolds (i.e., spun coat, large microfiber, and medium microfiber). Our analysis of the acquired terabyte-sized collection is motivated by the need to understand the nature of the shape dimensionality (1D vs 2D vs 3D) of cell-scaffold interactions relevant to tissue engineers that grow cells on biomaterial scaffolds.

resultsWe designed five statistical and three geometrical contact models, and then down-selected them to one from each category using a validation approach based on physically orthogonal measurements to CLSM. The two selected models were applied to 414 z-stacks with three scaffold types and all contact results were visually verified. A planar geometrical model for the spun coat scaffold type was validated from atomic force microscopy images by computing surface roughness of 52.35 nm ±31.76 nm which was 2 to 8 times smaller than the CLSM resolution. A cylindrical model for fiber scaffolds was validated from multi-view 2D scanning electron microscopy (SEM) images. The fiber scaffold segmentation error was assessed by comparing fiber diameters from SEM and CLSM to be between 0.46% to 3.8% of the SEM reference values. For contact verification, we constructed a web-based visual verification system with 414 pairs of images with cells and their segmentation results, and with 4968 movies with animated cell, scaffold, and contact overlays. Based on visual verification by three experts, we report the accuracy of cell segmentation to be 96.4% with 94.3% precision, and the accuracy of cell-scaffold contact for a statistical model to be 62.6% with 76.7% precision and for a geometrical model to be 93.5% with 87.6% precision.

conclusionsThe novelty of our approach lies in (1) representing cell-scaffold contact sites with statistical intensity and geometrical shape models, (2) designing a methodology for validating 3D geometrical contact models and (3) devising a mechanism for visual verification of hundreds of 3D measurements. The raw and processed data are publicly available from https://isg.nist.gov/deepzoomweb/data/ together with the web -based verification system.

Indexed as

Models, BiologicalAlgorithmsBiocompatible MaterialsBone Marrow CellsHumansImaging, Three-DimensionalInternetMaleMesenchymal Stem CellsMicroscopy, Atomic ForceMicroscopy, ConfocalMicroscopy, Electron, ScanningTissue ScaffoldsUser-Computer InterfaceX-Ray MicrotomographyYoung AdultBiocompatible MaterialsCell-scaffold contactCellular measurementsCo-localizationContact evaluationLarge-volume 3D image processingSegmentation modelsWeb-based verification

Identifiers

PMID29183290
PMCPMC5706418

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.